Scores of people told the UN that the National Directorate of Security (NDS) and the Afghan National Police had physically or mentally abused them, using beatings, electrocution and toenail removal, according to the report.
But the head of the UN in Afghanistan, Staffan de Mistura, said that torture was neither institutional nor government policy, and praised the ministry and intelligence agency for allowing access to their prisons for research.
The Afghan government rejected many of the allegations, but conceded there may have been some abuse, and added that steps were being taken to prevent further problems.
Interviews with 379 pre-trial detainees and convicted prisoners were conducted at 47 different facilities by the United Nations Assistance Mission in Afghanistan (UNAMA) from October 2010 to August 2011.
The report said 324 of the detainees were accused of crimes related to the war.
There was systematic torture found at five NDS "facilities", the report said, and "multiple, credible allegations" of torture at two others. There were also some allegations from 17 other facilities that the UN said it was still investigating.
Almost half of those interviewed were suspected insurgents, 20 percent were arrested while carrying explosives and 11 percent were failed suicide bombers.
UNAMA said almost half of those it interviewed at NDS facilities experienced interrogation techniques that constituted torture. Of those in police facilities, more than a third of the 117 suspected insurgents or those believed to be assisting militants told UNAMA they had been subjected to torture or inhumane treatment.
Beyond physical mistreatment, which included sexual humiliation, many prisoners also said they had been held beyond the maximum duration allowed by law and denied family visits.
The United Nations said Afghanistan's difficult security situation did not justify any mistreatment.
False claims, or insurgent propaganda?
The intelligence agency said in an official response that "reference has been made to some issues that are not in conformity with work principles of the NDS," and specifically rejected some allegations of mistreatment.
"Torture methods such as electric shock, threat of rape, twisting of sexual organs etc. are methods that are absolutely non-existent in the NDS," an official government response said.
The statement suggested some insurgent prisoners might be making false claims to discredit the government. However it also said several officials had recently been dismissed or suspended, and the agency was "keen for reform and improvement in the field of interrogation".
UNAMA said it had designed its study to take into account concerns from the Afghan authorities that detainees might give false accounts to discredit security agencies and further insurgent propaganda.
The Interior Ministry accepted there were cases of poor treatment of detainees in police custody, but said they were in the minority and it was committed to punishing violators and ensuring police were trained to protect human rights.
"It is evident ... that the outcome of the report cannot be totally rejected/denied due to some existing problems," it said.
The report follows a similar UN investigation into alleged torture that prompted NATO to halt transfers of prisoners to several southern Afghan jails in July.
Those findings raised questions about the capacity of Afghan security forces at a time when they are meant to be taking on greater security responsibilities ahead of a planned withdrawal of all foreign combat troops by the end of 2014.
COMMENTS (4)
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Karzai can even move his fingers out side his palace without US support.It means US is involved in the brutality.
We canNot expect less. This is all happening under the unberralla of USA. They use to call Taliban barbarian but look now. We do not see any much change in 10 years.
Where are the INDIAN extremist who come on this forum and comment against Pakistan.
After all the things the US has done in Afganistan what kind of fool would believe that the Karzai GOV & northern alliance represent the Afgan people. Only brainless morons can be fooled by the drama demostration in kabul orchestrated by CIA against ISI & PAK. But the sad truth is that majority of americans & secular muslims can be fooled this easily into believing everything the White house spokeman says.
Physical torture has never been a state policy in any of the world countries, yet incidents like Abu Ghureb scandals reveal periodically in the history. In Pakistan even a child is familiar with the classical "Chotarr" of our Pakistani Police.